Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:32 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the conclus package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/conclus.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 374/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
conclus 1.0.0 (landing page) Ilyess Rachedi
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: conclus |
Version: 1.0.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:conclus.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings conclus_1.0.0.tar.gz |
StartedAt: 2021-10-14 17:43:24 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 17:54:44 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 680.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: conclus.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:conclus.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings conclus_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/conclus.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘conclus/DESCRIPTION’ ... OK * this is package ‘conclus’ version ‘1.0.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘conclus’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed runCONCLUS 16.518 0.230 88.497 retrieveFromGEO 12.449 0.322 12.783 addClustering-scRNAseq 7.495 0.160 10.865 retrieveGenesInfo-scRNAseq 5.617 0.083 9.170 normaliseCountMatrix-scRNAseq 5.375 0.115 8.289 testClustering-scRNAseq 1.279 0.039 21.767 runDBSCAN-scRNAseq 0.434 0.010 18.594 clusterCellsInternal-scRNAseq 0.340 0.033 19.667 generateTSNECoordinates-scRNAseq 0.267 0.042 23.976 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test-all.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
conclus.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL conclus ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘conclus’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (conclus)
conclus.Rcheck/tests/test-all.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("testthat") > library("conclus") Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) > test_check("conclus") Min. 1st Qu. Median Mean 3rd Qu. Max. 1 1 1 1 1 1 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 277 ] > > proc.time() user system elapsed 45.344 1.389 124.390
conclus.Rcheck/conclus-Ex.timings
name | user | system | elapsed | |
addClustering-scRNAseq | 7.495 | 0.160 | 10.865 | |
calculateClustersSimilarity-scRNAseq | 0.089 | 0.001 | 0.090 | |
clusterCellsInternal-scRNAseq | 0.340 | 0.033 | 19.667 | |
conclusCacheClear | 0.001 | 0.001 | 0.000 | |
constructors | 0.020 | 0.005 | 0.024 | |
exportResults-scRNAseq | 0.177 | 0.047 | 0.224 | |
generateTSNECoordinates-scRNAseq | 0.267 | 0.042 | 23.976 | |
getters | 0.016 | 0.004 | 0.020 | |
loadDataOrMatrix | 0.011 | 0.003 | 0.014 | |
normaliseCountMatrix-scRNAseq | 5.375 | 0.115 | 8.289 | |
plotCellHeatmap | 0.125 | 0.003 | 0.128 | |
plotCellSimilarity-scRNAseq | 0.129 | 0.002 | 0.132 | |
plotClusteredTSNE-scRNAseq | 0.550 | 0.007 | 0.559 | |
plotClustersSimilarity | 0.099 | 0.002 | 0.102 | |
plotGeneExpression-scRNAseq | 0.223 | 0.002 | 0.226 | |
rankGenes-scRNAseq | 0.178 | 0.002 | 0.179 | |
retrieveFromGEO | 12.449 | 0.322 | 12.783 | |
retrieveGenesInfo-scRNAseq | 5.617 | 0.083 | 9.170 | |
retrieveTableClustersCells-scRNAseq | 0.029 | 0.001 | 0.030 | |
retrieveTopClustersMarkers-scRNAseq | 0.047 | 0.001 | 0.047 | |
runCONCLUS | 16.518 | 0.230 | 88.497 | |
runDBSCAN-scRNAseq | 0.434 | 0.010 | 18.594 | |
setters | 0.030 | 0.002 | 0.032 | |
testClustering-scRNAseq | 1.279 | 0.039 | 21.767 | |